We will develop the bridging technology to adapt our manual and automated microfluidic instruments to applications in cell-based assays. Our goal is to start with only slightly modified versions of instruments that we have already commercialized for DNA sequencing/forensics applications. We hope to exploit novel aspects of the existing parallel microfluidics and meso-format scanning confocal detection, to create new low-cost instruments for routine cell-based assays in the environment of the single-investigator biology lab. The large-frame BioMEMS-768 DNA sequencer becomes the starting point for an automated platform that, we will prove, outperforms FACS for a class of rare-cell, primary-cell and quantitative-marker applications. The desk-top-sized GeneTrack system will be the basis for an inexpensive semi-manual system, which, nonetheless, has sufficient throughput to support a major cloning screen. The development will be collaborative with neighboring laboratories at the Whitehead Institute (Lodish and Weinberg), as well as an MIT Laboratory of Wittrup, and the MGH laboratory of Bringhurst. These collaborators will run large-scale cloning screens and rare-cell assays though our instruments. As a moderate-risk extension, we will demonstrate deep epigenetic analysis by developing a means to read out highly multiplexed (50-100 gene) expression levels by reverse-transcription PCR on image-selected cell fractions. This will all be done in 384-lane parallelism by a novel real-time RT-PCR electrophoretic multiplexing method. The goal is to provide a powerful and multifunctional tool for biology.